Anova

On Sat, 2008-03-15 at 12:48 -0500, daniel jupiter wrote:

 > Hi all,
 >
 > I apologize for what might be a silly question.
 >
 > I am interested in doing a one way anova.
 > This is not too hard in and of itself, either with anova, aov or oneway.test
 > .
 >
 > However, I need to
 > 1) get pvalues,

 if obj is the result of anova, aov, oneway.test, then

 str(obj) ## for anova
 str(summary(obj)) ## for aov
 str(obj) ## for oneway.test

 to find the names of the elements of obj that contain the p-values of
 the various tests/models. In the first two you are looking for the
 component "Pr(>F)" and the latter is obvious ("p.value")

 For summary(aov) objects, the result is a list so this gets the p-value
 you need:

 obj[[1]]$`Pr(>F)` or obj[[1]][,5]]

 for anova then this:

 obj$`Pr(>F)` or obj[,5]

 note the quoting of the component name using backticks.

 For oneway.test

 obj$p.value

 > 2) do a posthoc analysis with Tukey HSD,

 ?TukeyHSD for the results of aov

 > 3) and have (sometimes) an unbalanced design.

 See ?lme in package nlme

 >
 > I just can't seem to put all the pieces together.
 >
 > Any suggestions?

 I'm not sure what the problem is here - you don't say. All of what I say
 above is documented in the relevant help pages for the various functions
 and using str() is a basic tenet of using R and looking at returned
 objects.

 Ok, you might have needed help with getting the p-values for some of
 those tests/models, but 2) and 3) are answered on ?aov

 For what you describe, stick with aov for balanced designs if you want
 to do TukeyHSD as there is a method for aov objects (otherwise) you'll
 need to refit the model.

 For unbalanced designs, check out lme and for that you may need to
 get/borrow the book by Pinhiero and Bates, reference details of which
 are given in item [7] on:

 http://www.r-project.org/doc/bib/R-books.html

 >
 > Thanks in advance,
 >
 > Dan.
 >

 HTH

 G
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